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Unable to defeat the Iron Giant using guns, tanks, or battleships, Kent Mansley suggest to General Rogard that they can destroy the Giant by using a nuclear missile from the USS Nautilus, which is sailing underwater near the city of Rockwell. General Rogard asks why they are going to bomb themselves to destroy the Giant, however Kent thinks the Giant can be lured out of the town, then destroyed. The General then agrees and orders one of his soldiers to contact the Nautilus to destroy the giant. The crew of the nuclear submarine then got the missile ready for fire.

After Hogarth brought the Giant back to his senses, Annie tells the U.S Army not to fire the missile from the Nautilus, as her son is still alive, and Dean explains to General Rogard that the Giant is friendly and is only retaliating as a result of the military’s actions. Ever defiant, Mansley’s still asserts that the Giant must be destroyed and tells Rogard that Dean’s claim is a trick to avoid the missile’s launching from the sub. However, the Giant shows up holding Hogarth in his hands to prove that he's not a threat, and upon realizing that Hogarth is still alive, Rogard tells his men to stand down. Rogard attempts to have the Nautilus aborted her missile launch for good in order not to make the same mistake again, but Mansley on the other hand, still assuming the Giant is a threat to the town, refuses to stand down and instead snatches the radio from Rogard and orders the Nautilus to launch the missile, the sub then fires its missile.

Shocked and infuriated, Rogard angrily informs Mansley that the missile is targeted to the Giant's current position, which will result not only the Giant's death, but in the destruction of Rockwell and its entire populous, when the missile re-enters the orbit. When Hogarth tells the robot about Rockwell's fate, the robot flies off and sacrifices himself to save the town by colliding with the missile, causing a massive explosion high up in the atmosphere. Both the town and the Nautilus are now safe.

USS Nautilus (SSN-571) was the world's first operational nuclear-powered submarine. The vessel was the first submarine to complete a submerged transit of the North Pole on 3 August 1958. Sharing names with Captain Nemo's fictional submarine in Jules Verne's Twenty Thousand Leagues Under the Sea, and named after another USS Nautilus (SS-168) that served with distinction in World War II, Nautilus was authorized in 1951 and launched in 1954. Because her nuclear propulsion allowed her to remain submerged far longer than diesel-electric submarines, she broke many records in her first years of operation, and traveled to locations previously beyond the limits of submarines. In operation, she revealed a number of limitations in her design and construction. This information was used to improve subsequent submarines.

Nautilus was decommissioned in 1980 and designated a National Historic Landmark in 1982. The submarine has been preserved as a submarine museum in Groton, Connecticut, where the vessel receives some 250,000 visitors a year.